Introduction to data science in R

Lesson 8: Putting it all together

Brian S. Evans, Ph.D.
Migratory Bird Center
Smithsonian Conservation Biology Institute

Setup for the lesson

# Load RCurl library:

library(RCurl)

# Load a source script:

script <-
  getURL(
    paste0(
      'https://raw.githubusercontent.com/bsevansunc/workshop_languageOfR/master/',
      'sourceCode_workshop.R'
    )
  )

# Evaluate then remove the source script:

eval(parse(text = script))

rm(script)

Today’s goals

Today’s goals

R Studio: Code sections

Code sections: Break larger file into discrete regions

• Improve workflow and readability
• Simplify code navigation
• Foldable

Insert section head:

# Section 1 

# Section 1 -----

# Section 1 ----*

R Studio: Code sections

Code sections: Break larger file into discrete regions

• Improve workflow and readability
• Simplify code navigation
• Foldable

Insert section head using CTRL(CMD)+SHIFT+R:

R Studio: Code sections

Code sections: Break larger file into discrete regions

• Improve workflow and readability
• Simplify code navigation
• Foldable

Insert section head: Ctrl(Cmd)+Shift+R:

R Studio: Code sections

Code sections: Break larger file into discrete regions

• Improve workflow and readability
• Simplify code navigation
• Foldable

R Studio: Code sections

Code sections: Break larger file into discrete regions

• Improve workflow and readability
• Simplify code navigation
• Foldable

R Studio: Code sections

Code sections: Break larger file into discrete regions

• Improve workflow and readability
• Simplify code navigation
• Foldable

Jump to: Shift+Alt+J

R Studio: Code sections

Code sections: Break larger file into discrete regions

• Improve workflow and readability
• Simplify code navigation
• Foldable

R Studio: Code sections

Code sections: Break larger file into discrete regions

• Improve workflow and readability
• Simplify code navigation
• Foldable

Fold all: Alt+O

R Studio: Code sections

Code sections: Break larger file into discrete regions

• Improve workflow and readability
• Simplify code navigation
• Foldable

Expand

R Studio: Code sections

Code sections: Break larger file into discrete regions

• Improve workflow and readability
• Simplify code navigation
• Foldable

Expand all: Shift+Alt+O

Exercise One:

Explore the code sections of the file sourceCode_workshop.R. Use this file to do the following:

1. The data frames birdCounts and birdMeasures are in the same code section. Provide separate code sections for each data frame.
2. Explore folding and unfolding these code sections.

R Studio: R Projects

R Studio: R Projects

R Studio: R Projects

R Studio: R Projects

Exercise Two:

Create a project in the directory where you are running the R files for this class.

R Studio: R Notebooks and Markdown

R Notebooks are digital lab notebooks written in Markdown, a plain text formatting language.

R Studio: R Notebooks and Markdown

R Notebooks are digital lab notebooks written in Markdown, a plain text formatting language.

R Studio: R Notebooks and Markdown

R Markdown documents

R Studio: R Notebooks and Markdown

R Markdown documents

R Studio: R Notebooks and Markdown

R Markdown documents

R Studio: R Notebooks and Markdown

R Markdown documents

R Studio: R Notebooks and Markdown

R Markdown documents

R Studio: R Notebooks and Markdown

R Markdown documents can also be written in html (like all of the presentations in this workshop).

Exercise Three:

Create a new R notebook. Copy-and-paste the code from the functions code section of sourceCodeWorkshop.R into the notebook document. Replace the comments with markdown text and wrap code sections for evaluation.

Sourcing code

Scripts called source code can be run from within another script.

• Use global source code for steps you run for every project
• Split large, multi-step projects into multiple scripts
1. Use project-level source code for long or multi-step projects
2. Connect scripts with source code

Sourcing code

Scripts called source code can be run from within another script.

• Use global source code for steps you run for every project
• Split large, multi-step projects into multiple scripts
1. Use project-level source code for long or multi-step projects
2. Connect scripts using sourcing

source('sourceCode_workshop.R')

Exercise Four:

1. Use the keyboard shortcut Ctrl(Cmd)+Shift+N to open a blank worksheet.
2. Copy-and-paste the following function into the worksheet:

printHw <- function(){
  "Hello world!"
}

3. Save the worksheet as sourceFunctions.R in your current working directory.
4. Use the function printHw to remove the function from your environment.
5. Type the following into your console:

source(`sourceFunctions.R`)

printHw()